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Subject:

No activation in 2nd level analysis

From:

Alexandra Fort <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 11 Aug 2004 09:43:47 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (343 lines)

Dear all,

I have run a problem using feat...
My study involves 10 subjects and 2 sessions for each subject with an
event-related design.

When I run a first level analyis (creating feats for each session,
registering to the standard template), all seems ok.

In a second level analysis, I try to combine session 1 and 2 of each subject
(input are lower level-feat directories) but here, I don't have any
activation whatever the subject or the contrast...

This lack of activation is very surprising since when I run the anaysis
before (my computer crashed and I loosed the data...) I get something at the
2nd and third level, so I guess I'm doing something wrong but what ...?

Any suggestions would be greatly appreciated...

Thank

Alexandra

------------------------------------------------

Here are the design for the 2nd level analysis tested for one subject:

# FEAT version number
set fmri(version) 5.1

# Analysis level
# 1 : First-level analysis
# 2 : Higher-level analysis
set fmri(level) 2

# Which stages to run
# 0 : No first-level analysis (registration and/or group stats only)
# 7 : Full first-level analysis
# 1 : Pre-Stats
# 3 : Pre-Stats + Stats
# 2 :             Stats
# 6 :             Stats + Contrasts, Thresholding, Rendering
# 4 :                     Contrasts, Thresholding, Rendering
set fmri(analysis) 6

# Delay before starting (hours)
set fmri(delay) 0

# Use relative filenames
set fmri(relative_yn) 0

# Balloon help
set fmri(help_yn) 1

# Run Featwatcher
set fmri(featwatcher_yn) 1

# Output directory
set fmri(outputdir) "/home/magnum/af/data/mri/MRdata/sub02-AB"

# TR(s)
set fmri(tr) 3

# Total volumes
set fmri(npts) 2

# Delete volumes
set fmri(ndelete) 0

# Number of first-level analyses
set fmri(multiple) 2

# Higher-level input type
# 1 : Inputs are lower-level FEAT directories
# 2 : Inputs are cope images from FEAT directories
set fmri(inputtype) 1

# Carry out pre-stats processing?
set fmri(filtering_yn) 0

# Brain/background threshold, %
set fmri(brain_thresh) 10

# Post-stats-only directory copying
# 0 : Overwrite original post-stats results
# 1 : Copy original FEAT directory for new Contrasts, Thresholding, Rendering
set fmri(newdir_yn) 0

# Slice timing correction
# 0 : None
# 1 : Regular up (0, 1, 2, 3, ...)
# 2 : Regular down
# 3 : Use slice order file
# 4 : Use slice timings file
# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
set fmri(st) 0

# Slice timings file
set fmri(st_file) ""

# Motion correction
# 0 : None
# 1 : MCFLIRT
set fmri(mc) 1

# Spin-history (currently obsolete)
set fmri(sh_yn) 0

# BET brain extraction
set fmri(bet_yn) 1

# Spatial smoothing FWHM (mm)
set fmri(smooth) 5

# Intensity normalization
set fmri(norm_yn) 0

# Highpass temporal filtering
set fmri(temphp_yn) 1

# Lowpass temporal filtering
set fmri(templp_yn) 0

# Carry out main stats?
set fmri(stats_yn) 1

# Carry out prewhitening?
set fmri(prewhiten_yn) 1

# Higher-level mixed effects choice
# 0 : Simple OLS
# 1 : FLAME (full)
# 2 : FLAME (stage 1 only)
set fmri(mixed_yn) 2

# Number of EVs
set fmri(evs_orig) 1
set fmri(evs_real) 1

# Number of contrasts
set fmri(ncon_orig) 1
set fmri(ncon_real) 1

# Number of F-tests
set fmri(nftests_orig) 0
set fmri(nftests_real) 0

# Add constant column to design matrix? (obsolete)
set fmri(constcol) 0

# Carry out post-stats steps?
set fmri(poststats_yn) 1

# Pre-threshold masking?
set fmri(threshmask) ""

# Thresholding
# 0 : None
# 1 : Uncorrected
# 2 : Voxel
# 3 : Cluster
set fmri(thresh) 3

# P threshold
set fmri(prob_thresh) 0.05

# Z threshold
set fmri(z_thresh) 1.8

# Z min/max for colour rendering
# 0 : Use actual Z min/max
# 1 : Use preset Z min/max
set fmri(zdisplay) 0

# Z min in colour rendering
set fmri(zmin) 1

# Z max in colour rendering
set fmri(zmax) 15

# Colour rendering type
# 0 : Solid blobs
# 1 : Transparent blobs
set fmri(rendertype) 1

# Background image for higher-level stats overlays
# 1 : Mean highres
# 2 : First highres
# 3 : Mean functional
# 4 : First functional
# 5 : Standard space template
set fmri(bgimage) 1

# Registration?
set fmri(reg_yn) 0

# B0 fieldmap unwarping?
set fmri(regunwarp_yn) 0

# Dwell/Asymmetry ratio
set fmri(dwellasym) -1

# Registration to initial structural
set fmri(reginitial_highres_yn) 0

# Search space for registration to initial structural
# 0   : No search
# 90  : Normal search
# 180 : Full search
set fmri(reginitial_highres_search) 90

# Degrees of Freedom for registration to initial structural
set fmri(reginitial_highres_dof) 12

# Do nonlinear registration to initial structural?
set fmri(reginitial_highres_nonlinear_yn) 0

# Registration to main structural
set fmri(reghighres_yn) 0

# Search space for registration to main structural
# 0   : No search
# 90  : Normal search
# 180 : Full search
set fmri(reghighres_search) 90

# Degrees of Freedom for registration to main structural
set fmri(reghighres_dof) 12

# Do nonlinear registration to main structural?
set fmri(reghighres_nonlinear_yn) 0

# Registration to standard image?
set fmri(regstandard_yn) 1

# Standard image
set fmri(regstandard) "/usr/local/fsl/rh-7.1/etc/standard/avg152T1_brain.hdr"

# Search space for registration to standard space
# 0   : No search
# 90  : Normal search
# 180 : Full search
set fmri(regstandard_search) 90

# Degrees of Freedom for registration to standard space
set fmri(regstandard_dof) 12

# Do nonlinear registration to standard space?
set fmri(regstandard_nonlinear_yn) 0

# High pass filter cutoff
set fmri(paradigm_hp) 100

# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 4

# Use lower-level cope 1 for higher-level analysis
set fmri(copeinput.1) 1

# Use lower-level cope 2 for higher-level analysis
set fmri(copeinput.2) 1

# Use lower-level cope 3 for higher-level analysis
set fmri(copeinput.3) 1

# Use lower-level cope 4 for higher-level analysis
set fmri(copeinput.4) 1

# 4D AVW data or FEAT directory (1)
set feat_files(1) "/home/magnum/af/data/mri/MRdata/sub02-run1.feat"

# 4D AVW data or FEAT directory (2)
set feat_files(2) "/home/magnum/af/data/mri/MRdata/sub02-run2.feat"

# Basic waveform shape (EV 1)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
set fmri(shape1) 2

# Convolution (EV 1)
# 0 : None
# 1 : Gaussian
# 2 : Gamma
# 3 : Double-Gamma HRF
# 4 : Gamma basis functions
# 5 : Sine basis functions
# 6 : FIR basis functions
set fmri(convolve1) 0

# Convolve phase (EV 1)
set fmri(convolve_phase1) 0

# Apply temporal filtering (EV 1)
set fmri(tempfilt_yn1) 0

# Add temporal derivative (EV 1)
set fmri(deriv_yn1) 0

# Custom EV file (EV 1)
set fmri(custom1) "dummy"

# Orthogonalise EV 1
set fmri(ortho1.0) 0

# Higher-level EV value for EV 1 and input 1
set fmri(evg1.1) 1

# Higher-level EV value for EV 1 and input 2
set fmri(evg2.1) 1

# Number of higher-level groups
set fmri(ngroups) 1

# Group membership for input 1
set fmri(groupmem.1) 1

# Group membership for input 2
set fmri(groupmem.2) 1

# Contrast & F-tests mode
# real : control real EVs
# orig : control original EVs
set fmri(con_mode_old) real
set fmri(con_mode) real

# Display images for contrast_real 1
set fmri(conpic_real.1) 1

# Title for contrast_real 1
set fmri(conname_real.1) "sub02"

# Real contrast_real vector 1 element 1
set fmri(con_real1.1) 1

# Contrast masking - use >0 instead of thresholding?
set fmri(conmask_zerothresh_yn) 0

# Do contrast masking at all?
set fmri(conmask1_1) 0

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